You can try to use suphp, so the web dir is writeable by the web server automatically. Right now, your problem is that:
Apache runs on www-data (or similar user).
The web tree is owned by another user.
You have to manually make some parts of the web home writeable for some of the CMS funcionality (for example, upload dirs)
With suphp, apache runs as the user that owns the executed script, so problems are gone.